Biomarkers Diagnostic Program

F E AT U R E D S P E A K E R S

C A M B R I D G E H E A L T H T E C H I N S T I T U T E ’ S 1 1 t h A N N U A L

The Leading Annual Meeting Dedicated to Biomarkers and Diagnostics Research and Implementation

MAY 5-7, 2015 | LOEWS PHILADELPHIA HOTEL | PHILADELPHIA, PA

W O R L D C O N G R E S S 2 0 1 5

BiomarkerWorldCongress.com

BIOMARKERS& DIAGNOSTICSFinal Agenda

M AY 5 - 6

Biomarkers for Patient Selection

Big Data for Personalized Medicine and Biomarker Discovery

Cell-Free Biomarkers and Diagnostics

Predictive Cancer Biomarkers

M AY 6 - 7

Companion Diagnostics

Clinical and Translational Biomarkers in Drug Discovery

Clinical NGS Testing

S H O R T C O U R S E S

Fit-for-Purpose Biomarker Assay Development and Validation

Next-Generation Sequencing as a Clinical Test

Register today and network with 400 of your colleagues

Raghu KalluriChair, Cancer BiologyMD Anderson Cancer Center

Nicholas C. DracopoliVice PresidentJohnson & Johnson

Marc LadanyiChair, Molecular OncologyMemorial Sloan-Kettering Cancer Center

Michael E. BurczynskiExecutive Director, BiomarkersBristol-Myers Squibb

Dennis J. SlamonChief, Hematology & OncologyUniversity of California, Los Angeles

Kenneth EmancipatorDirector, Companion DiagnosticsMerck Research Labs

Elaine LyonMedical DirectorARUP Laboratories

Alan T. WrightChief Medical OfficerRoche Diagnostics

Darrell R. BorgerDirector, Biomarker LaboratoryHarvard Medical School

Monica MotwaniPrecision Medicine LeaderAbbVie

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Organized by: Cambridge Healthtech Institute

Premier Sponsors:

C O N F E RE N C E AT - A - G L A N C E

T1: Biomarkers for Patient SelectionT2: Big Data for Personalized

Medicine and Biomarker DiscoveryT3: Cell-Free Biomarkers and

DiagnosticsT4: Predictive Cancer Biomarkers

Tuesday, May 5

7:00 am Conference Registration and Morning Coffee

8:00-10:10 Implementing Precision MedicineBig Data for Biomarker Discovery and Drug Development

Circulating Tumor DNA as Biomarkers and Diagnostics


10:10-10:40 Coffee Break in the Exhibit Hall with Poster Viewing

10:40-12:00 pm Implementing Precision Medicine (cont’d)Big Data for Biomarker Discovery and Drug Development (cont’d)

Circulating Tumor DNA as Biomarkers and Diagnostics (cont’d)

Circulating Tumor DNA as Biomarkers and Diagnostics (cont’d)

12:00-1:30 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

1:30-3:20 NGS for Biomarker Discovery and Patient Selection Big Data to Advance Personalized Medicine Exosomes and Microvesicles NGS for Biomarker Discovery and Patient Selection

3:20-4:10 Refreshment Break in the Exhibit Hall with Poster Viewing

4:10-5:00NGS for Biomarker Discovery and Patient Selection (cont’d)

Big Data to Advance Personalized Medicine (cont’d) Circulating Biomarkers in Drug DiscoveryNGS for Biomarker Discovery and Patient Selection (cont’d)

5:00-6:00 Welcome Reception in the Exhibit Hall with Poster Viewing

5:30 Short Course Registration

6:00-9:00 Dinner SC1: Fit-for-Purpose Biomarker Assay Development and Validation (*Separate registration required)

Wednesday, May 6

7:30 am Breakfast Presentations (Sponsorship Opportunities Available) or Morning Coffee

8:25-9:50 Predictive Cancer Biomarkers for Targeted Therapy Genomic Data Analysis microRNA and ncRNAPredictive Cancer Biomarkers for Targeted Therapy


10:45-12:00 pmPredictive Cancer Biomarkers for Targeted Therapy (cont’d)

Genomic Data Analysis (cont’d) microRNA and ncRNA (cont’d)Predictive Cancer Biomarkers for Targeted Therapy (cont’d)

12:00 Close of Conference

T5: Companion DiagnosticsT6: Clinical and Translational Biomarkers in Drug Discovery

T7: Clinical NGS Testing

11:00 am Conference Registration

12:15-1:30 pm Lunch on Your Own Luncheon Presentation Sponsored by Quanterix Luncheon Presentation Sponsored by NuGen

1:30-3:20Companion Diagnostics Development and Commercialization Strategies

Biomarkers in Drug Discovery Decision Making NGS in the Clinic

3:20-4:25 Refreshment Break in the Exhibit Hall with Poster Viewing

4:25-5:40Companion Diagnostics Development and Commercialization Strategies (cont’d)

Translational Biomarkers: From Discovery to the Clinic NGS in the Clinic (cont’d)


6:00-9:00 Dinner SC2*: Next-Generation Sequencing as a Clinical Test (*Separate registration required)

Thursday, May 7

7:30 am Breakfast Presentations (Sponsorship Opportunities Available) or Morning Coffee

8:25-9:50 Companion Diagnostics Case Studies Biomarker Assay Development and Validation NGS-Driven Clinical Trials


10:45-12:00 Companion Diagnostics Case Studies (cont’d) Genomic Biomarker Discovery NGS-Driven Clinical Trials (cont’d)

12:00-1:30 Lunch on Your Own

1:30-2:50 Partnering and Collaborations Partnering and Collaborations NGS Assay Development and Platforms


3 | BiomarkerWorldCongress.com

S P O N S O R S

Premier Sponsors

Corporate Sponsors

Corporate Support Sponsors


D I N N E R C O U R S E S *

Tuesday, May 5, 6:00-9:00 pm

SC1: Fit-for-Purpose Biomarker Assay Development and ValidationInstructors:John L. Allinson, FIBMS, Head, Biomarker Strategy, Drug Development Services, LGC GroupViswanath Devanarayan, Ph.D., Global Head & Senior Research Fellow, Exploratory Statistics & Bioinformatics, AbbVie, Inc.

This tutorial will provide recommendations on the “fit-for-purpose” best practices in the development and validation of biomarker assays for exploratory or advanced biomarker applications. Strategies for different applications at various phases of biomarker development will be described. Key elements in the method of development and validation will be illustrated with examples, including reference to standard material, sample stability and collection integrity, validation and QC samples, validity of reference standards, calibration curve fitting methods, method optimization and feasibility studies. Special challenges in protein biomarker assays will be discussed, including strategies for moving from biomarker panels in the exploratory phase to the few markers chosen to support clinical trials, cross-validation of biomarker assays, etc.

Outline:

• Introduction: Nomenclature, types of biomarker methods/assays, method development and validation road-map, fundamental validity, similarity and differences from PK assays and diagnostic applications

• Pre-analytical and bioanalytical elements: Target range, standards, validation and QC samples, stability, matrix effect, specificity and relative selectivity

• Calibration curve model selection, evaluation and weighting

• Method feasibility and optimization with precision profiles

• Evaluation of some pre-study validation characteristics such as precision, bias, sensitivity and quantification limits

• Use of sample controls for in-study performance monitoring and conformance testing among laboratories

• Special considerations for multiplex assays, cross-validation of assays, etc.

• Method comparisons

Wednesday, May 6, 6:00-9:00 pm

SC2: Next-Generation Sequencing as a Clinical TestInstructors:Seth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of MedicineAvni Santani, Ph.D., Assistant Professor, Clinical Pathology, University of Pennsylvania School of Medicine

Next-Generation Sequencing (NGS) is used widely in clinical research for the discovery of disease-associated genes, and the clinical community is beginning to embrace this technology for diagnostic testing. The rapid evolution of NGS technologies presents significant opportunities and challenges for researchers and clinicians for improving health outcomes, particularly with respect to an increased emphasis on personalized and preventive medicine. Adoption of NGS in the clinical laboratory setting requires the adoption of many processes and procedures, such as the analytic and clinical validation of the test, CLIA certification/CAP accreditation, standards for reference materials, availability for proficiency testing, and questions regarding reimbursement and informed consent. The success of NGS as a viable diagnostic modality depends on many branches of the health care community working together. This session will be informative and practical for the researcher and laboratorians who are considering launching NGS as a clinical test.

*Separate Registration Required.

BiomarkerWorldCongress.com | 4

D I S T I N G U I S H E D FAC U LT Y

John L. Allinson, FIBMS, Head, Biomarker Strategy, Drug Development Services, LGC Group

Jiri Aubrecht, Pharm.D., Ph.D., Senior Director and Safety Biomarker Group Lead, Drug Safety Research & Development, Pfizer

Nazneen Aziz, Ph.D., Chief Research Officer & Senior Vice President, Phoenix Children’s Hospital

Mark S. Boguski, M.D., Ph.D., Associate Professor, Center for Biomedical Informatics, Harvard Medical School

Darrell R. Borger, Ph.D., Director, Biomarker Laboratory, Massachusetts General Hospital and Harvard Medical School

Carrie Brodmerkel, Ph.D., Director, Immunology Biomarkers, Johnson & Johnson

Catherine Brownstein, Ph.D., Instructor, Pediatrics, Harvard Medical School and Boston Children’s Hospital

Kenneth Buetow, Ph.D., Director, Computational Sciences and Informatics Program for Complex Adaptive Systems; Professor, School of Life Sciences, Arizona State University

Michael E. (Ransom) Burczynski, Ph.D., Executive Director, Biomarker Technologies, Exploratory Clinical and Translational Research, Bristol-Myers Squibb

James Cai, Ph.D., Head, Data Science, Roche

Ken Chang, Ph.D., Clinical Assay Development & Outsourcing Lead, Merck

Clark Chen, M.D., Ph.D., Associate Professor and Chief, Stereotactic and Radiosurgery; Vice-Chairman, Academic Affairs, Neurosurgery, University of California, San Diego

Rong Chen, Ph.D., Director, Clinical Genome Informatics, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai

Seth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

Viswanath Devanarayan, Ph.D., Global Head & Senior Research Fellow, Exploratory Statistics & Bioinformatics, AbbVie, Inc.

Nicholas C. Dracopoli, Ph.D., Vice President, Janssen R&D, Johnson & Johnson

Paula Eason, Ph.D., Scientific Program Manager, Cancer Division of Research Partnerships, Foundation for the National Institutes of Health

Daniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling Core, National Cancer Institute, NIH

Kenneth Emancipator, M.D., Executive Medical Director, Molecular Biomarkers and Diagnostics, Merck Research Laboratories

Helen Fernandes, Ph.D., Associate Professor, Pathology and Laboratory Medicine, Weill Cornell Medical College

Andrea Ferreira-Gonzalez, Ph.D., Professor and Chair, Division of Molecular Diagnostics; Director, Molecular Diagnostics Laboratory, Department of Pathology, Virginia Commonwealth University

James M. Ford, M.D., Associate Professor, Medicine (Oncology) and Genetics; Director, Stanford Clinical Cancer Genomics Program, Stanford University School of Medicine

Yasuhiro Funahashi, Ph.D., Senior Director, Biomarkers and Personalized Medicine, Eisai

Birgit Funke, Ph.D., Assistant Professor, Pathology, MGH/Harvard Medical School; Director, Clinical Research and Development, Laboratory for Molecular Medicine, Partners HealthCare

Stephen T. Furlong, Ph.D., Safety Science Lead, AstraZeneca

Peter S. Gargalovic, Ph.D., Principal Scientist, Cardiovascular Drug Discovery Biology, Bristol-Myers Squibb

Jaya Goyal, Ph.D., Director, Translational Sciences, Value-Based Medicine, Biogen Idec

George A. Green IV, Ph.D., Group Director, Pharmacodiagnostic Center of Excellence, Bristol-Myers Squibb

Steven Gutman, M.D., Myraqa Strategic Advisor, Illumina, Inc.

Christos Hatzis, Ph.D., Assistant Professor, Medicine, and Director, Bioinformatics, Breast Medical Oncology, Yale University School of Medicine

Matthias Holdhoff, M.D., Ph.D., Assistant Professor, Oncology, Medicine and Neurosurgery, Brain Cancer Program, SKCCC, Johns Hopkins University

Xiaolan Hu, Ph.D., Head, Genetically Defined Diseases, Bristol-Myers Squibb

Chris Huang, Ph.D., Principal Scientist, Systems Pharmacology & Biomarkers, Immunology TA, Janssen R&D

Usman Iqbal, M.D., Senior Medical Affairs Leader, AstraZeneca

Shidong Jia, Ph.D., Scientist, Oncology Biomarker Development, Genentech

Bing-Hua Jiang, Ph.D., Professor, Pathology, Anatomy and Cell Biology, Thomas Jefferson University

Raghu Kalluri, M.D., Ph.D., Professor & Chair, Cancer Biology, MD Anderson Cancer Center

Ann Kapoun, Ph.D., Vice President, Translational Medicine, OncoMed Pharmaceuticals

Marc Ladanyi, M.D., William Ruane Chair in Molecular Oncology, Molecular Diagnostics Service and Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center

Andrea H. Lauber, Ph.D., Executive Director, Business Development, Clinical Biomarkers and Pharmacodiagnostics, Bristol-Myers Squibb

Eunice Lee, Ph.D., Division of Immunology and Hematology Devices, Office of In Vitro Diagnostics and Radiological Health, CDRH, FDA

Bin Li, Ph.D., Associate Director, Computational Biology, Takeda

Ming-Lin Liu, M.D., Ph.D., Research Assistant Professor, Dermatology, Perelman School of Medicine, University of Pennsylvania

Hui Ling, M.D., Ph.D., Odyssey Fellow, Experimental Therapeutics, MD Anderson Cancer Center

Tracy Lively, Ph.D., Deputy Associate Director, Cancer Diagnosis Program, National Cancer Institute, NIH

Johan Luthman, D.D.S., Ph.D., Vice President, Clinical Neuroscience, Eisai

Rajyalakshmi Luthra, Ph.D., Director, Molecular Diagnostic Laboratory; Professor, Pathology and Laboratory Medicine, MD Anderson Cancer Center

Elaine Lyon, Ph.D., Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Associate Professor, University of Utah School of Medicine; Past President, Association for Molecular Pathology

Subha Madhavan, Ph.D., Associate Professor and Director, Innovation Center for Biomedical Informatics; Director, Clinical Research Informatics, Lombardi Comprehensive Cancer Center, Georgetown University

G. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School

Shrikant Mane, Ph.D., Director, Yale Center for Genome Analysis

William B. Mattes, Ph.D., DABT, Director, Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration

Ron Mazumder, Ph.D., MBA, Global Head, R&D and Operations, Janssen Diagnostics, Janssen Pharmaceutical Companies of Johnson & Johnson

Ian McCaffery, Ph.D., Head, Companion Diagnostic Development, Genentech

Jason Merker, M.D., Ph.D., Assistant Professor, Pathology, Stanford University Medical Center

Jennifer J.D. Morrissette, Ph.D., Clinical Director, Center for Personalized Diagnostics, University of Pennsylvania School of Medicine

Monica Motwani, Ph.D., Translational Oncology & Precision Medicine Leader, Oncology Discovery, AbbVie

Aejaz Nasir, M.D., MPhil, Fellow, College of American Pathologists; Senior Medical Advisor & Surgical Pathology Lead, Molecular Solid Tumor & Anatomic Pathologist, Tailored Therapeutics, Diagnostic & Experimental Pathology, Eli Lilly and Company

James Novotny, Ph.D., Group Director, Pharmacodiagnostics, Bristol-Myers Squibb

Yoshiya Oda, Ph.D., President, Biomarkers and Personalized Medicine Core Function Unit, Eisai

Gregory J. Opiteck, Ph.D., Senior Principal Scientist, Merck

Nickolas Papadopoulos, Ph.D., Professor, Ludwig Center, SKCCC, Johns Hopkins University

Abhijit A. Patel, M.D., Ph.D., Assistant Professor, Therapeutic Radiology, Yale University School of Medicine

Suso Platero, Ph.D., Director, Oncology Biomarkers, Janssen Pharmaceuticals

Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity (an MPLN company)

Deepak Rajpal, Ph.D., Director, Computational Biology, GlaxoSmithKline

Mitch Raponi, Ph.D., Senior Director, Molecular Diagnostics, Clovis Oncology

Carolina Rizo, Ph.D., MBA, Director, Business Development, Roche Molecular Systems

Wolfgang Sadee, Dr.rer.nat., Professor & Director, College of Medicine Center for Pharmacogenomics, The Ohio State University

Avni Santani, Ph.D., Assistant Professor, Clinical Pathology, University of Pennsylvania School of Medicine

Nadeem Sarwar, Ph.D., Vice President & Global Head, Genetics & Human Biology, Eisai

Nikoletta Sidiropoulos, M.D., Medical Director, Genomic Medicine Program, University of Vermont

Dennis J. Slamon, M.D., Ph.D., Chief, Hematology & Oncology, The David Geffen School of Medicine, University of California, Los Angeles

David Smith, Ph.D., Professor, Laboratory Medicine & Pathology, Mayo Clinic

Sharon Sokolowski, MS, Senior Principal Scientist, Pfizer Global Research & Development

Joan Sopczynski, Ph.D., Senior Manager, Predictive Informatics, Business Insights, R&D Business Technology, Pfizer

George Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine and Pathology, Mayo Clinic

John A. Wagner, M.D., Ph.D., Senior Vice President & Head, Global Clinical and Translational Sciences, Takeda Pharmaceuticals

I-Ming Wang, Ph.D., Principal Scientist, Genetics and Pharmacogenomics, Merck Research Labs

Liling Warren, Ph.D., Senior Scientific Investigator, GlaxoSmithKline

Anton Wellstein, M.D., Ph.D., Professor, Oncology, Pharmacology and Medicine, Georgetown University Medical School; Associate Director, Basic Science, Lombardi Comprehensive Cancer Center

David T.W. Wong, D.M.D., DMSc, Felix & Mildred Yip Professor and Associate Dean of Research, UCLA School of Dentistry; Director, Center for Oral/Head & Neck Oncology Research

Alan T. Wright, M.D., CMO, Roche Diagnostics Corporation

Xuemei Zhao, Ph.D., Principal Scientist, Molecular Biomarkers and Diagnostics Laboratory, Merck

Zhongming Zhao, Ph.D., Professor, Biomedical Informatics, Cancer Biology and Psychiatry, Vanderbilt University School of Medicine

Biomarkers & Diagnostics World Congress 2015


HOTEL & TRAVEL I N FORMAT I ON

Conference Venue and Hotel:

Loews Philadelphia Hotel1200 Market StreetPhiladelphia, PA 19107Phone: 215-627-1200

Reservations: Go to the travel page of biomarkerworldcongress.com

Discounted Room Rate: $249 s/dDiscounted Cut-off Date: April 6, 2015

Go to the travel page of biomarkerworldcongress.com for additional information

CHI offers comprehensive sponsorship packages which include presentation opportunities, exhibit space, branding and networking with specific prospects. Sponsorship allows you to achieve your objectives before, during, and long after the event. Any sponsorship can be customized to meet your company’s needs and budget. Signing on early will allow you to maximize exposure to qualified decision-makers.

Podium Presentations — Available Within Main Agenda!

Showcase your solutions to a guaranteed, targeted audience. Package includes a 15- or 30-minute podium presentation within the scientific agenda, exhibit space, on-site branding, access to cooperative marketing efforts by CHI, and more.

Invitation-Only VIP Dinner/Hospitality Suite

Sponsors will select their top prospects from the conference pre-registration list for an evening of networking at the hotel or at a choice local venue. CHI will extend invitations and deliver prospects, helping you to make the most out of this invaluable opportunity. Evening will be customized according to sponsor’s objectives, i.e.:

• Purely social• Focus group• Reception style• Plated dinner with specific conversation focus

Breakfast & Luncheon Podium Presentations

Opportunity includes a 30-minute podium presentation. Boxed lunches are delivered into the main session room, which guarantees audience attendance and participation. A limited number of presentations are available for sponsorship and they will sell out quickly. Sign on early to secure your talk!

Exhibit

Exhibitors will enjoy facilitated networking opportunities with qualified delegates. Speak face-to-face with prospective clients and showcase your latest product, service, or solution.

Additional branding and promotional opportunities are available, including:

• Conference Tote Bags• Literature Distribution (Tote Bag Insert or Chair Drop)• Badge Lanyards• Program Guide Advertisement• Padfolios and More...

Looking for additional ways to drive leads to your sales team?

CHI’s Lead Generation Programs will help you obtain more targeted, quality leads throughout the year. We will mine our database of 800,000+ life science professionals to your specific needs. We guarantee a minimum of 100 leads per program! Opportunities include:

• Whitepapers • Web Symposia• Custom Market Research Surveys• Podcasts

Sponsorsh i p, E xh i b i t & Lead Generat ion Opportun it i es

For sponsorship and exhibit information, please contact:

Ilana Quigley | Sr. Business Development Manager781-972-5457 | [email protected]

BiomarkerWorldCongress.com | 6


Biomarkers for Patient Selection

M AY 5 - 6

TUESDAY, MAY 5


Implementing Precision Medicine8:00 Chairperson’s Opening RemarksAlan T. Wright, M.D., CMO, Roche Diagnostics Corporation

8:10 Companion Diagnostics – A New Take on Medical ValueAlan T. Wright, M.D., CMO, Roche Diagnostics CorporationCompanion diagnostics are proving value by targeting, monitoring and directing personalized therapies. In the future, companion diagnostics will expand to include both biochemical and physical measurements. Testing can be discrete, periodic or continuous with analyzers that may be remote, worn or implanted. Just as advancements in biochemistry and pharmacology have driven therapeutics, innovations in measurement techniques will revolutionize healthcare.

8:35 Understanding Disease Heterogeneity, Status, Trajectory and Treatment Response to Enable Patient StratificationJaya Goyal, Ph.D., Director, Translational Sciences, Value-Based Medicine, Biogen Idec

9:00 Quantitative Immunohistochemistry for Effective Breast Cancer Patient StratificationHallgeir Rui, M.D., Ph.D., Cancer Biology & Pathology, Thomas Jefferson University

9:25 Multiplexed Biomarkers: Transitioning from Discovery to the Clinic

Sponsored by

Robert Neely, Ph.D., Research Investigator, Bioanalytical Sciences, Bristol-Myers SquibbWith the developing need of multiple biomarkers in clinical programs, the need for multiplexed platforms has increased considerably. Multiplexing analytes will save time and sample; however, it will lead to an increase in analytical factors that will need to be assessed during method development and validation. The two most widely used platforms for multiple analyte screening are either a bead based or a planar format. This talk will focus on these platforms and highlight the technical challenges that can arise in a multiplex assay. Specifically, it will focus on the analytical rigor needed to transition from discovery to the clinic.

9:55 Q&A with the Speakers

10:10 Coffee Break in the Exhibit Hall with Poster Viewing

10:40 Precision Medicine and Biomarker Development at the NCITracy Lively, Ph.D., Deputy Associate Director, Cancer Diagnosis Program, National Cancer Institute, NIHThe development of predictive markers to guide the use of emerging targeted therapeutic agents requires new approaches to both clinical trials and correlative laboratory science. This talk will present NCI’s experience with novel trial designs, the Exceptional Responders initiative and more effective approaches to the integration of biomarker development into cancer therapy trials.

11:05 Talk Title to be AnnouncedCarrie Brodmerkel, Ph.D., Director, Immunology Biomarkers, Johnson & Johnson

11:30 Operationally Identifying Pharmacogenetic VariantsGregory J. Opiteck, Ph.D., Senior Principal Scientist, MerckMerck has undertaken an enterprise change management initiative to understand the sources of complexity and cost in identifying functionally relevant PGx variation. Finding the inflection points between cost and complexity was key. Merck has now moved to a fully standardized analytical platform which delivers consistent and high quality PGx data on a time scale that is impactful to the decision-making process. Therefore, we are in keeping with a customer-centric model, while reducing demands on operational processes and information systems.

12:00 pm Luncheon Presentation: Role of Biomarkers in Improving the Success Rate of Early Oncology Drug Development

Sponsored by

Kamala Maddali, DVM, Ph.D., Director, Scientific Development, Quest Diagnostics Clinical TrialsBiomarkers have contributed to the advancement of targeted therapies and the rise of personalized medicine which optimize the probability of success in early oncology drug development. This presentation will cover various oncology case studies on the role of biomarkers: in patient selection strategies including Companion Diagnostics to stratify patients who will benefit from the clinical trial, as predictive biomarkers to predict patient outcomes, and in predicting toxicity, efficacy, and drug dosage to ensure that critical endpoints are achieved.

NGS for Biomarker Discovery and Patient Selection

1:30 Chairperson’s RemarksNazneen Aziz, Ph.D., Chief Research Officer & Senior Vice President, Phoenix Children’s Hospital

1:35 Application of NGS for Biomarker Discovery and Patient SelectionXiaolan Hu, Ph.D., Head, Genetically Defined Diseases, Bristol-Myers Squibb

2:00 Phoenix Children’s Hospital to Address the Unmet Need: Slow Progress in Pediatric Drug DevelopmentNazneen Aziz, Ph.D., Chief Research Officer & Senior Vice President, Phoenix Children’s HospitalThe need for new drugs in pediatric cancer is acute. Virtually no new therapy has been introduced in the past two decades. Treatment for relapsed patients is lower than in adults yet a large number of childhood cancer patients will relapse. In stark contrast to the rapid introduction of targeted therapies in adults more effective therapies are unavailable in pediatric cancer. PCH will focus on genomic analysis to better understand disease mechanisms to develop new therapeutics for pediatric cancer.

2:25 A General Approach to the Discovery and Translation of Multi-Gene Biomarkers in Drug Discovery and TherapyWolfgang Sadee, Dr.rer.nat., Professor & Director, College of Medicine Center for Pharmacogenomics, The Ohio State UniversityExtensive genetics/genomics studies have yet to account for the estimated heritability of complex traits, including diseases and their treatments. Our discovery pipeline encompasses detailed molecular genetics of target genes – to avoid use of surrogate markers – and large-scale data analytics to reveal phenotype associations involving gene-gene-environment interactions. Discovering frequent regulatory variants in key genes often under positive selection, we are now in a position to develop clinically relevant biomarker panels, demonstrated with examples.


2:50 A Novel Phospho-Proteomic Diagnostic for Patient Stratification and Therapy Selection for Breast Cancer

Sponsored by

Glenn Hoke, Ph.D., Executive Vice President and COO, Theranostics Health™, Inc.The TheraLink® Assay for Breast Cancer, a commercially available CAP/CLIA test, measures the proteomic signature in patient’s cancer, to provide the activation status for multiple drug targets. Designed for use in the routine clinical setting, this molecular diagnostic assay can identify which patients are more likely to respond to a particular molecularly targeted therapy. Case studies and the design of a prospective trial will be presented.

3:20 Refreshment Break in the Exhibit Hall with Poster Viewing

4:10 Utility of Targeted NGS Panels for Cancer in an Academic Molecular Pathology LaboratoryHelen Fernandes, Ph.D., Associate Professor, Pathology and Laboratory Medicine, Weill Cornell Medical CollegeThe utility of targeted next-generation sequencing-based assays for identification of genomic variants has made significant advances in the field of molecular oncology. Testing panels and platforms have enabled clinical molecular pathology laboratories to expand their testing menu to include NGS assays that can provide information for a more reliable prediction of personalized cancer therapies. Additionally, the assays can identify relevant genes that may have implications for enrollment of the patient in clinical trials. This presentation will focus on the issues involved for optimal performance and implementation characteristics of assays for the identification of somatic variants in solid tumors in an academic molecular pathology laboratory.

4:35 Patient Stratification in Oncology Using NGS: An Application of the PATH™ Analytics Platform to AML Patients from TCGA

Sponsored by

Scott Marshall, Ph.D., Managing Director, Analytics, Precision for MedicineMolecular heterogeneity in tumors is expected to impact prognosis and response to therapy, and the ability to stratify patients based on their underlying molecular profiles can improve outcomes. The transformation of high-dimensional genomic data into personalized treatments requires cutting-edge science and advanced analytics. To help biopharmaceutical companies realize this goal, Precision for Medicine has developed the PATH™ Analytics Platform, a multi-modal platform designed to accelerate research on biomarker discovery and patient stratification by combining advanced Bayesian analytics and real-time data exploration.



6:00-9:00 pm Dinner Short Course*SC1: Fit-for-Purpose Biomarker Assay Development and Validation

*Separate registration required

WEDNESDAY, MAY 6

7:30 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

Predictive Cancer Biomarkers for Targeted Therapy8:25 Chairperson’s RemarksGeorge Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine and Pathology, Mayo Clinic

8:30 Use of Biomarkers for Decision-Making in Breast Cancer TherapyDennis J. Slamon, M.D., Ph.D., Chief, Hematology & Oncology, The David Geffen School of Medicine, University of California, Los Angeles

8:55 The Impact of Multiplexed Genotyping in Directing Cancer Care and a Role for Combining Genotype with Histology for Biomarker DiscoveryDarrell R. Borger, Ph.D., Director, Biomarker Laboratory, Massachusetts General Hospital and Harvard Medical SchoolOur laboratory has conducted clinical genotyping in a large academic hospital for 7 years, and we have started to evaluate its impact on expanding targeted therapy options for cancer patients. With the integration of next-generation sequencing technologies, more complex genotypes are now being identified. Subsequently, the integration of histological testing may provide important perspective into the biological function of unknown variants and the ability to identify new biomarkers of response.

9:20 From Discovery Through Commercialization of Personalized Multiplex Biomarker Assays

Sponsored by

Al Akowitz, Ph.D., Vice President, Strategic Sales, Meso Scale Discovery


10:45 Genomic Markers Associated with Pathologic Complete Response and Resistance in Triple Negative Breast CancerChristos Hatzis, Ph.D., Assistant Professor, Medicine, and Director, Bioinformatics, Breast Medical Oncology, Yale University School of MedicineEfforts to develop transcriptional predictors of chemotherapy sensitivity in triple negative breast cancer (TNBC) have been met with limited success due to the heterogeneity of this disease. We explored whether genomic differences in the exomes of extremely chemotherapy sensitive and highly chemotherapy resistant TNBC cases could provide clues of chemosensitivity. Although a few genes show response-associated mutational patterns, the chemoresistant cases appear to have higher mutational load and subclonal heterogeneity, suggesting that higher DNA diversity may be associated with chemotherapy resistance. Interestingly, resistant tumors show characteristic mutational spectrum shifts that may suggest heterogeneous branch evolution. These broad measures of genomic diversity could show promise as markers of resistance to chemotherapy.

11:10 Comprehensive Translational Research to Identify Predictive Biomarkers of Lenvatinib in the Preclinical and Clinical StudyYasuhiro Funahashi, Ph.D., Senior Director, Biomarkers and Personalized Medicine, EisaiThis presentation will cover: 1) systems biology to identify biomarker candidates for Lenvatinib using the cancer cell line panel, 2) translational research to test biomarker candidates in multiple Phase II trials, and 3) biomarker correlative analysis in Phase III trial.

11:35 Identification of Independent Primary Lung Tumors and Intrapulmonary Metastases Using DNA JunctionsGeorge Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine and Pathology, Mayo ClinicDistinguishing independent primary tumors from intrapulmonary metastases in non-small-cell carcinoma remains a clinical dilemma with significant clinical implications. Using next-generation DNA sequencing, we developed a chromosomal rearrangement-based approach to differentiate multiple primary tumors from metastasis. Tumor specimens from patients with known independent primary tumors and metastatic lesions were used for lineage test development, which was then applied to multifocal cases. Lung tumors predicted to be independent primary tumors based on different histologic subtype did not share any genomic rearrangements. In cases of lung primary tumor and paired distant metastasis, shared rearrangements were identified in all cases, emphasizing the patient specificity of identified breakpoints. Concordance between histology and genomic data occurred in the majority of cases. Discrepant cases were resolved by genome sequencing. A diagnostic lineage test based on genomic rearrangements from mate-pair sequencing demonstrates promise for distinguishing independent primary from metastatic disease in lung cancer.

12:00 pm Close of Conference


Big Data for Personalized Medicine and Biomarker Discovery

M AY 5 - 6

TUESDAY, MAY 5


Big Data in Biomarker Discovery and Drug Development

8:00 Chairperson’s Opening RemarksNicholas C. Dracopoli, Ph.D., Vice President, Janssen R&D, Johnson & Johnson

8:10 Big Data and Small Trials: Translating Biological Data into Clinical BiomarkersNicholas C. Dracopoli, Ph.D., Vice President, Janssen R&D, Johnson & JohnsonAll of the companion diagnostic tests approved by the FDA for use in oncology are for “driver mutations” in genes involved in signal transduction pathways. These tests are for single analytes predicting the functional status of the drug target or pathway. There are no approved companion diagnostics for drugs that work through alternative mechanisms such as chemotherapy or immunomodulation. This presentation will discuss why so few biomarkers have been developed and why we have mostly failed to develop molecular profiles that predict drug response.

8:35 Applying Data Science in Translational Clinical ResearchJames Cai, Ph.D., Head, Data Science, RocheThe intelligent use of Big Data has transformed many industries. It also presents numerous opportunities for pharmaceutical companies as we collect more genomic Big Data directly from patients. In this talk I will outline a Data Science model that emphasizes mixed-capability teams and impact on science and business decisions. I will discuss how quantitative analytical skills, agile programming, novel technologies and business acumen all contribute to this model. I will illustrate with examples where Data Science was applied to clinical research resulting in new scientific insights and better business decisions.

9:00 Using Clinical and Real World Data for Biomarker Discovery in Precision MedicineJoan Sopczynski, Ph.D., Senior Manager, Predictive Informatics, Business Insights, R&D Business Technology, PfizerReal world and clinical trial databases consist of large patient data sets that can be explored for biological insights. Examples will be presented describing the analysis of this patient data for biomarker identification and disease knowledge. Methods used to analyze the data, including the application of machine learning techniques, will be described highlighting their ability to identify biomarkers distinguishing patient populations.

9:25 Biology Driven Strategies to Discover Novel Biomarkers and Predictive Markers from Genomic Sequencing Data

Sponsored by

Ashley Van Zeeland, Ph.D., CEO, Cypher GenomicsThe adoption of genomic sequencing beyond targeted panels in clinical development has been impeded by the difficulty of discovering a signal from the noise in small clinical studies. This presentation will describe, and present results from, a comprehensive, biology-based approach that can identify novel biomarkers from whole exome or whole genome sequencing data from the small sample sizes that are typical of drug development and lead to the development of novel companion diagnostic products.



10:40 Building and Leveraging “Clinical and EHR Data Stack” to Optimize Clinical Development and Patient OutcomesUsman Iqbal, M.D., Senior Medical Affairs Leader, AstraZenecaBig Data analysis of clinical outcomes, genetic profiles and tissue morphology is a big driver of personalized medicine. However, different elements of Big Data have different applications and considerations in personalized medicine. This presentation will focus on the development and application of the Real World Evidence category of Big Data and how innovative platforms linking clinical and EHRs platform can strategically optimize patient segmentation, clinical development and health outcomes.

11:05 Exploring Clinical Transcriptomics for BiomarkersDeepak Rajpal, Ph.D., Director, Computational Biology, GlaxoSmithKlineWe will share our experience from a case study on clinical transcriptomics in a dermatology indication space to understand disease resolution following therapeutic intervention.

11:30 Translational Biomarker Identification for Patient Stratification and Disease Indication Selection through Big DataBin Li, Ph.D., Associate Director, Computational Biology, TakedaWe implemented a tranSmart-based translational infrastructure, with globally normalized molecular profiling data (~1600 GEO studies) and manually curated patient information (~200 GEO studies). Also, a PLSR-based modeling framework was designed and implemented, using a special splitting strategy and canonical pathways to capture robust information for biomarker discovery. Combining these efforts, we were able to build drug-sensitivity predictive models for SOC drugs, and to successfully re-predict these drugs’ FDA-approved cancer indications.

12:00 pm Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

Big Data to Advance Personalized Medicine1:30 Chairperson’s RemarksRong Chen, Ph.D., Director, Clinical Genome Informatics, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai

1:35 The Opportunities and Challenges of Biomarker-Driven, Targeted TherapiesMark S. Boguski, M.D., Ph.D., Associate Professor, Center for Biomedical Informatics, Harvard Medical School

2:00 Using Big Data to Interpret Personal Genomes for Disease Variant Discovery, Precision Medicine and Novel TherapeuticsRong Chen, Ph.D., Director, Clinical Genome Informatics, Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiHundreds of thousands of individuals have been sequenced and released into public repositories, providing an exciting resource for the discovery of disease variants and therapeutic targets. This presentation will describe how we built a knowledge base through 100,000 exomes, millions of literatures, protein structures, and post-translational modification sites, and developed applications to interpret sequencing cohorts and biobank data for disease variant discovery, diagnosis and novel therapeutics. I will discuss how we interpret exomes and RNA-Seq data for personalized cancer therapeutic reports.

2:25 Data Science Platforms for Molecularly-Targeted Therapy and Personalized Medicine ResearchSubha Madhavan, Ph.D., Associate Professor and Director, Innovation Center for Biomedical Informatics; Director, Clinical Research Informatics, Lombardi Comprehensive Cancer Center, Georgetown UniversityG-DOC Plus is an enhanced web platform that uses cloud computing and other


advanced computational tools to handle NGS and medical images so that they can be analyzed in the full context of other omics and clinical information to drive personalized medicine research. G-DOC Plus tools have been leveraged in the cancer and non-cancer realms for hypothesis generation in precision medicine and translational research.

2:50 The Developmental Neuropsychiatry Program at BCH: Using Big Data for Personalized Medicine and Biomarker DiscoveryCatherine Brownstein, Ph.D., Instructor, Pediatrics, Harvard Medical School and Boston Children’s HospitalBoston Children’s Hospital is developing the infrastructure needed for large-scale psychiatric research and treatment discovery with the creation of the Developmental Neuropsychiatry Program (DNP). This new center is in a unique position to improve psychiatric care through precision genetic medicine. The DNP is working towards faster and more accurate diagnosis through assessment of a patient’s phenotype, MRI results and neurophysiology, in combination with next-generation sequencing and gene discovery. The goal is targeted prescribing and increased possibilities for investigational therapies. The DNP is investigating therapeutics to prevent schizophrenia by working with the youngest patients, creating neuronal cell cultures to identify cell autonomous effects, and constructing models of neural networks. The DNP also has cutting-edge research in assessing response to medication and outcomes in the context of their genotype and phenotype. The Clinical Pharmacogenomics Program is working with the Psychiatry Department to study the relationship between genotype and reported adverse drug reactions. Another research study is enrolling patients to identify behavioral and brain biomarkers linked to psychotic illness. Finally, groundbreaking research out of two Harvard laboratories has created a novel all-optical electrophysiology platform to rapidly screen drugs for functional effects in human neurons.


4:10 Catalyzing Delivery of Novel and Targeted Therapeutics from Human Genetics to PatientsJanna Hutz, Ph.D., Director and Head, Quantitative Genetics and Bioinformatics, Eisai

4:35 Realizing Personalized Medicine through Application of a Next-Generation Cyber Capability to See the Emergent Whole in Big DataKenneth Buetow, Ph.D., Director, Computational Sciences and Informatics Program for Complex Adaptive Systems; Professor, School of Life Sciences, Arizona State UniversityData Science has the capacity to provide the needed “tools” to tackle the unique challenges generated by personalized medicine. Arizona State University’s (ASU) Complex Adaptive Systems team is building a first generation Data Science research platform – the Next Generation Cyber Capability (NGCC). The ASU NGCC – composed of hardware, software and people – transforms “Big Data” to information and creates the evidence necessary to enable personalized medicine. The NGCC permits data “points” to be evaluated in concert using Big Data analytic frameworks thereby identifying an emergent, coherent “whole.” Biologic network analysis represents one such promising integrative approach. These networks account for the individual heterogeneity in underlying etiology as well as the interaction of diverse events necessary to generate complex phenotypes.





WEDNESDAY, MAY 6


Genomic Data Analysis8:25 Chairperson’s RemarksShrikant Mane, Ph.D., Director, Yale Center for Genome Analysis

8:30 Big Data Experiment – What Does Whole Genome Sequencing Tell Us?Chris Huang, Ph.D., Principal Scientist, Systems Pharmacology & Biomarkers, Immunology TA, Janssen R&D

8:55 Hypothesis-Free Versus Hypothesis-Driven Approaches to Predictive Modeling of Genomic DataViswanath Devanarayan, Ph.D., Global Head & Senior Research Fellow, Exploratory Statistics & Bioinformatics, AbbVie, Inc.Modeling of genomics Big Data to predict phenotypes of interest typically involved a variety of machine/statistical-learning methods. Hypothesis-free approach entails taking a totally unbiased approach by building the optimal predictive signatures from the whole genome data. Hypothesis-driven approaches tend to focus the predictive modeling efforts to only a subset of the whole genome that is previously known to be implicated to the phenotype, for example, from disease and target based pathway analysis. We will compare the results and relative benefits from these two approaches using traditional microarray as well as RNA-Seq data from neuroblastoma patients.

9:20 Application of Next-Generation Sequencing to Identify Actionable Mutations and Cancer Driver GenesZhongming Zhao, Ph.D., Professor, Biomedical Informatics, Cancer Biology and Psychiatry, Vanderbilt University School of MedicineNext-generation sequencing (NGS) technologies have enabled investigators to sequence thousands of tumor genomes. Correspondingly, personal genomics and personalized medicine is emerging as a new research field. In this talk, I will first present the identification of actionable mutations through our melanoma whole genome sequencing and characterization of mutational changes associated with drug resistance in EGFR-mutant lung cancer cell lines. Then, I will introduce our recently developed bioinformatics methods for identification of cancer genes from NGS data.


10:45 Systems Genetics Approaches in Drug DiscoveryPeter S. Gargalovic, Ph.D., Principal Scientist, Cardiovascular Drug Discovery Biology, Bristol-Myers SquibbEvolution of high-throughput analytical methodologies and lowering of the cost is now allowing an unprecedented access to genomic and phenotypic information across large clinical and pre-clinical population studies. Today R&D is faced with a challenge to implement effective ways to leverage the available population data and provide guidance for drug discovery and development. Systems genetics is emerging as a novel “cutting edge” approach to interrogate complex disease population data. This presentation will highlight the concepts and show examples of its application to drug discovery.

11:10 Recent Advancement in Mendelian Genomics and Data Management at Yale Center for Genome AnalysisShrikant Mane, Ph.D., Director, Yale Center for Genome AnalysisThe Yale Center for Genome Analysis (YCGA) is one of the leaders in the identification of disease-causing DNA variants. In the last four years, the use of next-gen sequencing has led to the publication of >150 articles in peer-reviewed journals including >25 in high-profile journals such as Science, Nature, Cell, New England Journal of Medicine and Nature Genetics, reporting new variants in various disorders, including hypertension, autism, several types of cancers, Gaucher disease, skin disorders and cortical malfunctions, all using exome analysis. In 2010, YCGA became part of the NHGRI supported Yale Center for Mendelian Genomics (YCMG), which is one of three centers in the U.S. that together form the Centers for Mendelian Genomics. The primary goal of this consortium is to use NGS and computational approaches to discover the genes and variants that underlie Mendelian conditions on a collaborative basis and at no cost to the investigator. The presentation will focus on recent discoveries made at YCGA, its computer infrastructure and the current challenges and solutions developed for data analysis and management.




Cell-Free Biomarkers and Diagnostics

M AY 5 - 6

TUESDAY, MAY 5



8:00 Chairperson’s Opening RemarksG. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School

8:10 Talk Title to be AnnouncedMatthias Holdhoff, M.D., Ph.D., Assistant Professor, Oncology, Medicine and Neurosurgery, Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins

8:35 Detection of Somatic Mutations in Biological Fluids in the Management of CancerNickolas Papadopoulos, Ph.D., Professor, Ludwig Center, SKCCC, Johns Hopkins UniversitySomatic mutations are cancer-specific biomarkers that reveal the presence of cancer when present in cell-free DNA or DNA derived from biological fluids. The number of circulating tumor DNA molecules with somatic mutations is very low compared to that of DNA molecules with wild type sequence and requires very sensitive methods for their detection. Here we discuss our efforts for developing such methods, studies for their validation, and their clinical applications.

9:00 cfDNA Ultra-Rare Allele Detection and DiscoverySeth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

9:25 Presentation to be Announced Sponsored by



10:40 Ultrasensitive Measurement of Circulating Tumor DNA to Assess Treatment Response and ResistanceAbhijit A. Patel, M.D., Ph.D., Assistant Professor, Therapeutic Radiology, Yale University School of MedicineOur group has developed an ultrasensitive, multi-target assay that can identify and quantify mutant ctDNA using novel error-suppression techniques applied to next-generation sequencing data. Broad coverage of mutation hotspots and warm-spots allows detection of ctDNA without prior knowledge of the tumor’s mutation profile. Clinical examples will be presented in which this approach is used to noninvasively monitor changes in ctDNA levels in response to treatment and to track the emergence of mutations that confer resistance to targeted therapies.

11:05 Single-Tube Enrichment of Mutations in Cancer Gene Panels from Circulating DNA, Using COLD-PCR Prior to Targeted Amplicon ResequencingG. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolTargeted re-sequencing of mutations in cancer-relevant genes provides opportunities for fine-tuning cancer therapy and follow-up during treatment, by examining mutations in tumors and bio-fluids. However, a major technical

limitation has been the lack of sensitivity of cancer re-sequencing panels for mutations below 1-2% abundance, which is frequently the case for circulating DNA. We present a newly developed method via which mutations in numerous amplicons are first enriched via COLD-PCR in a single-tube reaction, prior to targeted re-sequencing. Using this approach, mutations of 0.01-0.1% abundance can be detected via next-generation sequencing.

11:30 Panel DiscussionModerator: G. Mike Makrigiorgos, Harvard Medical School


Exosomes and Microvesicles1:30 Chairperson’s RemarksRaghu Kalluri, M.D., Ph.D., Professor & Chair, Cancer Biology, MD Anderson Cancer Center

1:35 The Biology and Functional Contribution of Exosomes in Cancer Progression and MetastasisRaghu Kalluri, M.D., Ph.D., Professor & Chair, Cancer Biology, MD Anderson Cancer Center

2:00 Characterization of Endothelial Microvesicles in Preclinical Species and Application to Drug DevelopmentSharon Sokolowski, MS, Senior Principal Scientist, Pfizer Global Research & DevelopmentMicrovesicles (0.5 – 1µM) in the peripheral blood of preclinical species have been evaluated as potential biomarkers of vascular perturbation or injury. Validation steps were completed to more fully characterize and understand the changes observed in peripheral blood microvesicle absolute counts in normal, dosed and diseased animals. While taking into consideration the advantages and caveats of microvesicle evaluation with current methods and instrumentation, application of microvesicles as safety and efficacy biomarkers during drug development was explored.

2:25 Extracellular Vesicles (EV) as a Molecular Diagnostic PlatformClark Chen, M.D., Ph.D., Associate Professor and Chief, Stereotactic and Radiosurgery; Vice-Chairman, Academic Affairs, Neurosurgery, University of California, San DiegoExtracellular vesicles (EVs) are cell-secreted vesicles that range 30-2,000 nm in size. These vesicles are secreted by both normal and neoplastic cells. Physiologically, EVs serve multiple critical biologic functions, including cellular remodeling, intracellular communication, modulation of the tumor microenvironment, and regulation of immune function. Because EVs contain genetic and proteomic contents that reflect the cell of origin, it is possible to detect tumor-specific material in EVs secreted by cancer cells. Importantly, EVs secreted by cancer cells transgress anatomic compartments and can be detected in the blood, cerebrospinal fluid and other bio-fluids of cancer patients. In this context, there is a growing interest in analyzing EVs from the bio-fluid of cancer patients as a means of disease diagnosis and therapeutic monitoring. This talk will focus on the development of EVs as a diagnostic platform for the most common form of brain cancer, glioblastoma, and discuss potential clinical translational opportunities.

2:50 Novel Role of Microvesicles in Cardiovascular DiseasesMing-Lin Liu, M.D., Ph.D., Research Assistant Professor, Dermatology, Perelman School of Medicine, University of Pennslyvania



Circulating Biomarkers in Drug Development4:10 Translational Circulating Biomarker Research for Drug DevelopmentYoshiya Oda, Ph.D., President, Biomarkers and Personalized Medicine Core Function Unit, EisaiBiomarkers can play very important roles for drug development because biomarkers can show the data for target engagement, target modulation, patient stratification and drug efficacy. As a sample source of biomarkers, tissue is an issue, because the amount of tissue is very limited and it is hard to obtain biopsy samples in certain disease areas. Circulating biomarkers in serum/plasma are very practical and patient-friendly. Several real examples about proteins, lipids and miRNAs as circulating biomarkers will be shown during the presentation.

4:35 Next Generation Sequencing of Circulating Tumor Cells from the CELLSEARCH® System

Sponsored by

Charles Saginario, Scientist, CRS Labs, Janssen Diagnostics





WEDNESDAY, MAY 6


microRNA and ncRNA8:25 Chairperson’s RemarksDavid T.W. Wong, D.M.D., DMSc, Felix & Mildred Yip Professor and Associate Dean of Research, UCLA School of Dentistry; Director, Center for Oral/Head & Neck Oncology Research

8:30 Application of miR-Based Biomarkers in Diagnosis and Management of Liver Injury in Human SubjectsJiri Aubrecht, Pharm.D., Ph.D., Senior Director and Safety Biomarker Group Lead, Drug Safety Research & Development, Pfizer

8:55 3’UTR SNPs that are Targets for A-I RNA Editing Control IGF1R mRNA Expression Levels in High-Risk NeuroblastomaDanika Johnston, Ph.D., Research Associate, The Children’s Hospital of Philadelphia

9:20 Exploration of Circulating Non-Coding RNAs as Cancer BiomarkersHui Ling, M.D., Ph.D., Odyssey Fellow, Experimental Therapeutics, MD Anderson Cancer Center


10:45 Salivary Extracellular Non-Coding RNA BiomarkersDavid T.W. Wong, D.M.D., DMSc, Felix & Mildred Yip Professor and Associate Dean of Research, UCLA School of Dentistry; Director, Center for Oral/Head & Neck Oncology ResearchExtracellular RNAs (exRNAs) in human bodily fluids are emerging as effective biomarkers for detection of diseases. Saliva, as the most accessible and non-invasive bodily fluid, has been shown to harbor exRNA biomarkers for human diseases including cancer. Using high-throughput RNA-Seq, we conducted an in-depth bioinformatic analysis of non-coding RNAs (ncRNAs) in human cell free saliva (CFS) of healthy subjects with a focus on microRNAs (miRNAs), piwi-interacting RNAs (piRNAs) and circular RNAs (circRNAs) reporting the unusual abundance of piRNA and the first demonstration of circRNA in a bodily fluid.

11:10 MicroRNAs in Mediating Tumor Angiogenesis, Drug Resistance and Autophagy Responses in Human CancersBing-Hua Jiang, Ph.D., Professor, Pathology, Anatomy and Cell Biology, Thomas Jefferson UniversityOur recent study demonstrates that a number of microRNAs (miRNAs) are downregulated in several kinds of human cancers including ovarian, breast, lung, colon and glioma; and that levels of miRNA suppression are associated with cancer development and drug resistance. To understand the mechanism, we found that several different kinds of miRNAs are involved in tumor growth, angiogenesis, drug resistance and autophagy responses through HER2, EGFR, IGF-IR and ATG14 pathways. The miRNA suppression is regulated by DNA methylation and reactive oxygen species.

11:35 Liquid Biopsies to Monitor Disease Progression and Therapeutic Response in CancerAnton Wellstein, M.D., Ph.D., Professor, Oncology, Pharmacology and Medicine, Georgetown University Medical School; Associate Director, Basic Science, Lombardi Comprehensive Cancer CenterClinically detectable cancer should be considered as a systemic disease. Cancer tissue analysis provides a snapshot of the makeup of the local disease and/or metastases that is limited by physical access to cancerous sites. In contrast, serial blood samples provide a source of biomarkers that can reveal real-time changes due to altered disease stage and/or treatment responses. The utility of circulating microRNAs will be discussed.



Predictive Cancer Biomarkers

M AY 5 - 6

TUESDAY, MAY 5



8:00 Chairperson’s Opening RemarksG. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School

8:10 Talk Title to be AnnouncedMatthias Holdhoff, M.D., Ph.D., Assistant Professor, Oncology, Medicine and Neurosurgery, Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins

8:35 Detection of Somatic Mutations in Biological Fluids in the Management of CancerNickolas Papadopoulos, Ph.D., Professor, Ludwig Center, SKCCC, Johns Hopkins UniversitySomatic mutations are cancer specific biomarkers that reveal the presence of cancer when present in cell-free DNA or DNA derived from biological fluids. The number of circulating tumor DNA molecules with somatic mutations is very low compared to that of DNA molecules with wild-type sequence and requires very sensitive methods for their detection. Here we discuss our efforts for developing such methods, studies for their validation, and their clinical applications.

9:00 cfDNA Ultra-Rare Allele Detection and DiscoverySeth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

9:25 Pharmacodynamic Assessment of Drug Response by Monitoring Mutational Load in Urinary Circulating Tumor DNA

Sponsored by

Mark Erlander, Ph.D., CSO, TrovageneThe concept of liquid biopsies is expanding to include urine as a specimen type. Using Precision Cancer MonitoringSM (PCM) platform for quantitative ctDNA analysis at a single copy level, we demonstrate that drug-induced immediate early changes in ctDNA mutational load correlate with tumor burden and treatment response. As a non-invasive specimen, urine enables frequent monitoring of ctDNA, and this accessibility can be applied to investigating mechanisms of action of targeted therapeutics and, ultimately, cancer management.



10:40 Ultrasensitive Measurement of Circulating Tumor DNA to Assess Treatment Response and ResistanceAbhijit A. Patel, M.D., Ph.D., Assistant Professor, Therapeutic Radiology, Yale University School of MedicineOur group has developed an ultrasensitive, multi-target assay that can identify and quantify mutant ctDNA using novel error-suppression techniques applied to next-generation sequencing data. Broad coverage of mutation hotspots and warm-spots allows detection of ctDNA without prior knowledge of the tumor’s mutation profile. Clinical examples will be presented in which this approach is used to noninvasively monitor changes in ctDNA levels in response to treatment and to track the emergence of mutations that confer resistance to targeted therapies.

11:05 Single-Tube Enrichment of Mutations in Cancer Gene Panels from Circulating DNA, Using COLD-PCR Prior to Targeted Amplicon ResequencingG. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical SchoolTargeted re-sequencing of mutations in cancer-relevant genes provides opportunities for fine-tuning cancer therapy and follow-up during treatment, by examining mutations in tumors and bio-fluids. However, a major technical limitation has been the lack of sensitivity of cancer re-sequencing panels for mutations below 1-2% abundance, which is frequently the case for circulating DNA. We present a newly developed method via which mutations in numerous amplicons are first enriched via COLD-PCR in a single-tube reaction, prior to targeted re-sequencing. Using this approach, mutations of 0.01-0.1% abundance can be detected via next-generation sequencing.

11:30 Panel DiscussionModerator: G. Mike Makrigiorgos, Harvard Medical School


NGS for Biomarker Discovery and Patient Selection1:30 Chairperson’s RemarksNazneen Aziz, Ph.D., Chief Research Officer & Senior Vice President, Phoenix Children’s Hospital

1:35 Application of NGS for Biomarker Discovery and Patient SelectionXiaolan Hu, Ph.D., Head, Genetically Defined Diseases, Bristol-Myers Squibb

2:00 Phoenix Children’s Hospital to Address the Unmet Need: Slow Progress in Pediatric Drug DevelopmentNazneen Aziz, Ph.D., Chief Research Officer & Senior Vice President, Phoenix Children’s HospitalThe need for new drugs in pediatric cancer is acute. Virtually no new therapy has been introduced in the past two decades. Treatment for relapsed patients is lower than in adults yet a large number of childhood cancer patients will relapse. In stark contrast to the rapid introduction of targeted therapies in adults more effective therapies are unavailable in pediatric cancer. PCH will focus on genomic analysis to better understand disease mechanisms to develop new therapeutics for pediatric cancer.

2:25 A General Approach to the Discovery and Translation of Multi-Gene Biomarkers in Drug Discovery and TherapyWolfgang Sadee, Dr.rer.nat., Professor & Director, College of Medicine Center for Pharmacogenomics, The Ohio State UniversityExtensive genetics/genomics studies have yet to account for the estimated heritability of complex traits, including diseases and their treatments. Our discovery pipeline encompasses detailed molecular genetics of target genes – to avoid use of surrogate markers – and large-scale data analytics to reveal phenotype associations involving gene-gene-environment interactions. Discovering frequent regulatory variants in key genes often under positive selection, we are now in a position to develop clinically relevant biomarker panels, demonstrated with examples.


2:50 A Novel Phospho-Proteomic Diagnostic for Patient Stratification and Therapy Selection for Breast Cancer

Sponsored by

Glenn Hoke, Ph.D., Executive Vice President and COO, Theranostics Health™, Inc.


4:10 Utility of Targeted NGS Panels for Cancer in an Academic Molecular Pathology LaboratoryHelen Fernandes, Ph.D., Associate Professor, Pathology and Laboratory Medicine, Weill Cornell Medical CollegeThe utility of targeted next-generation sequencing-based assays for identification of genomic variants has made significant advances in the field of molecular oncology. Testing panels and platforms have enabled clinical molecular pathology laboratories to expand their testing menu to include NGS assays that can provide information for a more reliable prediction of personalized cancer therapies. Additionally, the assays can identify relevant genes that may have implications for enrollment of the patient in clinical trials. This presentation will focus on the issues involved for optimal performance and implementation characteristics of assays for the identification of somatic variants in solid tumors in an academic molecular pathology laboratory.

4:35 Patient Stratification in Oncology Using NGS: An Application of the PATH™ Analytics Platform to AML Patients from TCGA

Sponsored by

Scott Marshall, Ph.D., Managing Director, Analytics, Precision for MedicineMolecular heterogeneity in tumors is expected to impact prognosis and response to therapy, and the ability to stratify patients based on their underlying molecular profiles can improve outcomes. The transformation of high-dimensional genomic data into personalized treatments requires cutting-edge science and advanced analytics. To help biopharmaceutical companies realize this goal, Precision for Medicine has developed the PATH™ Analytics Platform, a multi-modal platform designed to accelerate research on biomarker discovery and patient stratification by combining advanced Bayesian analytics and real-time data exploration.





WEDNESDAY, MAY 6


Predictive Cancer Biomarkers for Targeted Therapy8:25 Chairperson’s RemarksGeorge Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine and Pathology, Mayo Clinic

8:30 Use of Biomarkers for Decision-Making in Breast Cancer TherapyDennis J. Slamon, M.D., Ph.D., Chief, Hematology & Oncology, The David Geffen School of Medicine, University of California, Los Angeles

8:55 The Impact of Multiplexed Genotyping in Directing Cancer Care and a Role for Combining Genotype with Histology for Biomarker DiscoveryDarrell R. Borger, Ph.D., Director, Biomarker Laboratory, Massachusetts General Hospital and Harvard Medical SchoolOur laboratory has conducted clinical genotyping in a large academic hospital

for 7 years, and we have started to evaluate its impact on expanding targeted therapy options for cancer patients. With the integration of next-generation sequencing technologies, more complex genotypes are now being identified. Subsequently, the integration of histological testing may provide important perspective into the biological function of unknown variants and the ability to identify new biomarkers of response.

9:20 From Discovery Through Commercialization of Personalized Multiplex Biomarker Assays

Sponsored by

Al Akowitz, Ph.D., Vice President, Strategic Sales, Meso Scale Discovery


10:45 Genomic Markers Associated with Pathologic Complete Response and Resistance in Triple Negative Breast CancerChristos Hatzis, Ph.D., Assistant Professor, Medicine; Director, Bioinformatics, Breast Medical Oncology, Yale University School of MedicineEfforts to develop transcriptional predictors of chemotherapy sensitivity in triple negative breast cancer (TNBC) have been met with limited success due to the heterogeneity of this disease. We explored whether genomic differences in the exomes of extremely chemotherapy sensitive and highly chemotherapy resistant TNBC cases could provide clues of chemosensitivity. Although a few genes show response-associated mutational patterns, the chemoresistant cases appear to have higher mutational load and subclonal heterogeneity, suggesting that higher DNA diversity may be associated with chemotherapy resistance. Interestingly, resistant tumors show characteristic mutational spectrum shifts that may suggest heterogeneous branch evolution. These broad measures of genomic diversity could show promise as markers of resistance to chemotherapy.

11:10 Comprehensive Translational Research to Identify Predictive Biomarkers of Lenvatinib in the Preclinical and Clinical StudyYasuhiro Funahashi, Ph.D., Senior Director, Biomarkers and Personalized Medicine, EisaiThis presentation will cover: 1) systems biology to identify biomarker candidates for Lenvatinib using the cancer cell line panel, 2) translational research to test biomarker candidates in multiple Phase II trials, and 3) biomarker correlative analysis in Phase III trial.

11:35 Identification of Independent Primary Lung Tumors and Intrapulmonary Metastases Using DNA JunctionsGeorge Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine and Pathology, Mayo ClinicDistinguishing independent primary tumors from intrapulmonary metastases in non-small-cell carcinoma remains a clinical dilemma with significant clinical implications. Using next-generation DNA sequencing, we developed a chromosomal rearrangement-based approach to differentiate multiple primary tumors from metastasis. Tumor specimens from patients with known independent primary tumors and metastatic lesions were used for lineage test development, which was then applied to multifocal cases. Lung tumors predicted to be independent primary tumors based on different histologic subtype did not share any genomic rearrangements. In cases of lung primary tumor and paired distant metastasis, shared rearrangements were identified in all cases, emphasizing the patient specificity of identified breakpoints. Concordance between histology and genomic data occurred in the majority of cases. Discrepant cases were resolved by genome sequencing. A diagnostic lineage test based on genomic rearrangements from mate-pair sequencing demonstrates promise for distinguishing independent primary from metastatic disease in lung cancer.



Companion Diagnostics

M AY 6 - 7

WEDNESDAY, MAY 6


12:15 pm Lunch on Your Own

Companion Diagnostics Development and Commercialization Strategies

1:30 Chairperson’s Opening RemarksKenneth Emancipator, M.D., Executive Medical Director, Molecular Biomarkers and Diagnostics, Merck Research Laboratories

1:35 Making Disciplined Decisions in Companion Diagnostic Development Using Clinical Epidemiologic TechniquesKenneth Emancipator, M.D., Executive Medical Director, Molecular Biomarkers and Diagnostics, Merck Research LaboratoriesChoosing which biomarker to develop as a companion diagnostic, choosing a cutoff, and even deciding whether or not a companion diagnostic should be co-developed with a therapeutic often provokes spirited discussions within pharmaceutical companies. However, these discussions need not involve high drama. This presentation will demonstrate a few simple, well-established clinical epidemiologic techniques which can guide rational, disciplined decisions. Examples of the application of these techniques will also be presented.

2:00 The Role of Companion Diagnostics in Improving Patient CareCarolina Rizo, Ph.D., MBA, Director, Business Development, Roche Molecular SystemsCompanion diagnostics is becoming a key element in cancer treatment. In this talk, I will: 1) discuss the importance of standardized testing due to variability observed in EQA schemes, 2) review the differences in test methodologies and the resulting impact on patient selection, 3) describe the value of clinical validation with a CDx and advantages it may bring to the drug registration process, and 4) evaluate how future technologies (liquid biopsies) may play a role in patient selection and management. I will show how companion diagnostics is improving patient care and will continue doing so.

2:25 Dollars and Sense: Making the Most of Companion DiagnosticsSteven Gutman, M.D., Myraqa Strategic Advisor, Illumina, Inc.Companion diagnostics are now commonly being evaluated early in the drug development process as important tools to reduce the cost of clinical trials and to improve study outcomes. These tests are also being used to ensure the clinically effective and cost effective use of new drugs. FDA review of these products appears to be flexible and “least burdensome” and third party payers generally have been willing to pay for these tests although not at the same premium as for drugs. With this background in mind, this talk will address the gaps that exist in the value proposition for companion diagnostics.

2:50 Diagnostics Partnering to Realize Combined Drug-Diagnostics Strategies Rolf Ehrnström, Scientific Advisor, Diagnostics Partnering, Thermo Fisher Scientific

Sponsored by


4:25 Tissue and Time: Perspectives on Companion Diagnostic DevelopmentRon Mazumder, Ph.D., MBA, Global Head, R&D and Operations, Janssen Diagnostics, Janssen Pharmaceutical Companies of Johnson & Johnson

4:50 Companion Diagnostics – Immunoassay and Other “Wet” Markers – Method Development and Choice of Platform – Challenges and ConsiderationsJohn L. Allinson, FIBMS, Head, Biomarker Strategy, Drug Development Services, LGC GroupThis talk will look at potential development of companion diagnostics in the “wet” biomarker space. Consideration will be given to: 1) range of analytical platforms available and factors that influence their choice, 2) development program from original research method through to accredited diagnostic – the technical challenges and requirements, 3) different applications of the research and diagnostic assays during a drug development program, and 4) overall project design – requirements from the sponsor, diagnostic and contract research organization to deliver a successful outcome.

5:15 Regulatory Perspective on in vitro Companion Diagnostic DevicesEunice Lee, Ph.D., Division of Immunology and Hematology Devices, Office of In Vitro Diagnostics and Radiological Health, CDRH, FDASince the approval of the HercepTest in 1998, significant strides have been made to establish a regulatory structure for companion diagnostic devices in the US. Companion diagnostics are defined as devices that provide information that is essential for the safe and effective use of a corresponding therapeutic. I will describe the current regulatory model for companion diagnostics, and share some lessons learned from successful co-development programs from the device perspective. My talk will also highlight considerations for validating the performance of in vitro diagnostics, and discuss potential challenges to the regulatory model for companion diagnostics in the future.


6:00-9:00 pm Dinner Short Course*SC2: Next-Generation Sequencing as a Clinical Test


THURSDAY, MAY 7

7:30am Breakfast Presentation: Next Generation in Situ Hybridization (ISH) and Immunohistochemistry (IHC)

Sponsored by

Sven Müller, Ph.D., Manager, R&D, ISH pharmDx, Dako - an Agilent Technology companyThe need for solid tumor biomarkers to be confirmed in context of tissue morphology calls for routine involvement of slide based techniques like IHC and ISH. The major drawbacks of these methods relates to a qualitative readout and a slow turn-around time, respectively. Based on Dako, an Agilent Technologies Company’s long term IHC and ISH expertise we are bringing these technologies to the next level, enabling us to continue being a One Stop Shop in IHC and ISH solutions for pharma partners - from early development to IVD class III kits. The symposium focuses on game changing improvements of the ISH and IHC technologies.

Companion Diagnostics Case Studies8:25 Chairperson’s RemarksJames Novotny, Ph.D., Group Director, Pharmacodiagnostics, Bristol-Myers Squibb


8:30 Translational and Companion Diagnostic Strategies: A Case Study of Development of a PI3K-Beta InhibitorMonica Motwani, Ph.D., Director, Precision Medicine & Diagnostics, GlaxoSmithKlineIn the era of precision medicine, efficient development and implementation of biomarker and companion diagnostic strategies in clinical studies is a key to being successful. This talk will discuss the PI3K beta inhibitor development as an example to illustrate various steps in the development and implementation of these strategies in clinic.

8:55 Evaluation of PD-L1 as a Potential Companion Diagnostic for Nivolumab, a Novel Immune Checkpoint Inhibitor for the Treatment of CancerJames Novotny, Ph.D., Group Director, Pharmacodiagnostics, Bristol-Myers SquibbPD-L1 expression has been documented on a wide variety of solid tumors, and PD-L1 positivity may correlate with response from treatment with PD-1 pathway inhibitors. Nivolumab is a fully human IgG4 PD-1 immune checkpoint inhibitor antibody that selectively prevents interaction with PD-L1 and PD-L2, thereby inhibiting the downregulation of antitumor T cell function. BMS has engaged in a comprehensive analytical and clinical evaluation of PD-L1 expression by IHC in order to determine the association between expression and clinical outcome for Nivolumab.

9:20 A New Paradigm for Precision Oncology: A Shared Vision for Universal Oncology Testing

Sponsored by

John Leite, Ph.D., Vice President, Oncology Market Development, Oncology, IlluminaThe rapid evolution of high-accuracy and high-throughput genomic technologies has created unprecedented opportunities for translational and clinical applications in cancer. Next-generation sequencing approaches now allow the interrogation of germline and somatic variation associated with malignancy across DNA and RNA sequence, structural variation, and epigenetic changes in many tissue types including blood. Potential applications span the continuum of cancer care, from inherited risk assessment and early detection to prediction of treatment response and recurrence monitoring.


10:45 Talk Title to be AnnouncedIan McCaffery, Ph.D., Head, Companion Diagnostic Development, Genentech

11:10 Development of a Homologous Recombination Deficiency (HRD) Companion Diagnostic Test for Selecting High Grade Ovarian Cancer Patients Likely to Respond to the PARP Inhibitor RucaparibMitch Raponi, Ph.D., Senior Director, Molecular Diagnostics, Clovis OncologyPARP inhibitors are active in patients whose tumors exhibit homologous recombination deficiency (HRD), and pathogenic mutations in the tumor suppressor gene BRCA (a key player in the HR pathway) is a predictor of PARPi efficacy. However, multiple mechanisms can result in HRD, which in turn leads to a BRCAness phenotype. A comprehensive genomic sequencing-based HRD test has been developed to identify a patient population who will benefit from

the PARP inhibitor Rucaparib. This approach is being prospectively tested in the ARIEL (Assessment of Rucaparib In ovarian cancEr triaLs) program and will be described.

11:35 Developing Biomarkers for Use in Patient Selection in Early Phase Clinical TrialsAnn Kapoun, Ph.D., Vice President, Translational Medicine, OncoMed PharmaceuticalsThis presentation will cover: 1) incorporating predictive biomarkers into early stage R&D to ensure each clinical candidate has a complimentary biomarker when it reaches the clinic, 2) embedding personalized medicine strategies into drug discovery to fast-track CDx programs, and 3) prospective and retrospective predictive biomarker case studies for Anti-Notch1 and for Tarextumab clinical programs.

12:00 pm Enjoy Lunch on Your Own

Partnering and Collaborations1:30 Chairperson’s RemarksGeorge A. Green IV, Ph.D., Group Director, Pharmacodiagnostic Center of Excellence, Bristol-Myers Squibb

1:35 Creating and Managing the Multiple Interfaces of Drug/Diagnostic Co-DevelopmentGeorge A. Green IV, Ph.D., Group Director, Pharmacodiagnostic Center of Excellence, Bristol-Myers SquibbAndrea H. Lauber, Ph.D., Executive Director, Business Development, Clinical Biomarkers and Pharmacodiagnostics, Bristol-Myers SquibbMany pharmaceutical companies are using an external partnering model to pursue co-development of drugs and diagnostic products. This approach provides access to diverse biomarkers, technology and platforms, as well as diagnostic manufacturing and commercialization expertise, thus maximizing diagnostic development capabilities. External partnering creates multiple interfaces of functions both within and between the drug and diagnostic companies. We will explore some of the challenges that accompany these interfaces, their management and implications, along with ideas for optimizing the “virtual diagnostic company” model for the Rx/Dx co-development environment.

2:25 Innovative Strategies and Progress in Translational Biomarkers in Clinical Oncology through Public-Private PartnershipsPaula Eason, Ph.D., Scientific Program Manager, Cancer Division of Research Partnerships, Foundation for the National Institutes of HealthThe continual need for development of biomarkers with robust clinical utility is an ongoing challenge for all cancer types. Incorporation of prognostic and predictive biomarkers into clinical trial strategies and therapeutic decision-making is essential to disentangle the complexities of the pathogenic process, drug pharmacodynamics, and tumor heterogeneity. Success will require strategic partnerships and alliances between public and private sectors to share resources, risks, experience and expertise, and to align multiple stakeholder incentives to support and accelerate sustainable innovation.


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Clinical and Translational Biomarkers in Drug Discovery

M AY 6 - 7

WEDNESDAY, MAY 6


12:15 pm Luncheon Presentation: Ultrasensitive Multiplexed Cytokine Measurements Sponsored by

Mark Roskey, Ph.D., Vice President & General Manager, Applications and Reagents, Quanterix CorporationThe normal healthy range for many cytokines is very close to the limit of detection of conventional immunoassay measurement techniques. Ultra-sensitive Simoa technology measures biomarkers in blood at extremely low levels of detection, allowing researchers to measure both healthy and sick subjects with confidence. Multiplex cytokine panels allow users to achieve similar sensitivity with each marker in a multiplex panel as they would if they were to test individual assays.

Biomarkers in Drug Discovery Decision-Making1:30 Chairperson’s Opening RemarksMichael E. (Ransom) Burczynski, Ph.D., Executive Director, Biomarker Technologies, Exploratory Clinical and Translational Research, Bristol-Myers Squibb

1:35 Enabling Robust Biomarker-Driven Decision-Making in Drug Development: Key Factors and ConsiderationsMichael E. (Ransom) Burczynski, Ph.D., Executive Director, Biomarker Technologies, Exploratory Clinical and Translational Research, Bristol-Myers SquibbProspective biomarker testing strategies in the clinic benefit from multiple perspectives including those of discovery biologists, translational scientists, biomarker technologists, physicians, statisticians, bioinformaticians and operational personnel. Studies designed from these perspectives enable teams to combine biomarker data across platforms from sufficiently powered, feasible-to-execute clinical studies that can potentially 1) elucidate disease pathophysiology, 2) confirm mechanism of action, 3) demonstrate target engagement, 4) confirm dose-dependent pharmacodynamic effects and even 5) determine if efficacy/safety profiles are enhanced in certain molecularly defined subsets of patients. In addition, judicious sampling in those same studies for future exploratory research can ultimately yield a biorepository of great value for identifying new disease indications, drug targets, biomarkers and other value-added information to the R&D organization in the future. Early definition of the biomarker strategy, coupled with a system that permits flexible re-evaluation of the strategy in light of new information, provides an optimal scenario for executing biomarker studies in the clinic. Finally, committing to objectively assessing each biomarker study’s success and impact in the overall decision-making around a candidate drug’s development permits a return-on-investment (ROI) calculation that can help refine future biomarker strategies to ensure only the most highly informative biomarker approaches and methodologies are employed. The present talk will review the basic tenets of a robust biomarker evaluation process and illustrate several biomarker study approaches in this paradigm that have led to rapid data generation, analysis and interpretation to support key decisions during the early clinical development of candidate therapies.

2:00 Who Owns Biomarker Qualification and Surrogate Endpoints?John A. Wagner, M.D., Ph.D., Senior Vice President & Head, Global Clinical and Translational Sciences, Takeda Pharmaceuticals

2:25 Talk Title to be AnnouncedSuso Platero, Ph.D., Director, Oncology Biomarkers, Janssen Pharmaceuticals

2:50 Ultrasensitive Measurement of IL-17 in Psoriasis PatientsCathy Soderstrom, Senior Scientist, Regulated Biomarkers Group, Pfizer Groton

Sponsored by


Translational Biomarkers: From Discovery to the Clinic

4:25 Chairperson’s RemarksJohan Luthman, D.D.S., Ph.D., Vice President, Clinical Neuroscience, Eisai

4:30 Current Status for AD Biomarkers: From Mice to Men to Trials and Clinical PracticeJohan Luthman, D.D.S., Ph.D., Vice President, Clinical Neuroscience, EisaiAlzheimer’s disease (AD) is a clear illustration of the introduction of biomarkers that has entirely changed the way drug R&D is executed, but also shows the challenges of addressing remaining hurdles. In AD research, biomarkers are now applied to translate animal data to early clinical studies, as well as to both identify and stage the disease in clinical trials. For example, biomarkers have become critical for diagnosis of AD pre-dementia. Moreover, demonstration of the presence of AD pathology using biomarkers has become central for drug trial stratification and enrichment strategies. Several modalities of AD biomarkers, imaging (e.g. MRI and PET), bio-fluid (e.g. CSF measures) and functional, are available for which there are different, but also commonly overlapping applications. At the same time, for many AD biomarkers considerable work remains in obtaining sufficient data on assay performance, clinical qualification for the intended context of use, standardization of use and regulatory approval before one can fully implement them in clinical trials and practice. In addition, it is also important to note the possibilities for operational implementation as well as the general acceptance and commercial potential of various AD biomarker modalities varies considerably. Commonly there are also differing opinions between academic and industrial scientists and regulators of what constitutes satisfactory validation and qualification for use of AD biomarkers as stand-alone or companion diagnostics, or as supportive outcome measures in clinical trials.

4:55 Approaches to Biomarkers that can “Translate the Stubbornness of Fortune”William B. Mattes, Ph.D., DABT, Director, Division of Systems Biology, National Center for Toxicological Research, US Food and Drug AdministrationThe terms “biomarker” and “translational” are all too often abused buzzwords; to have practical meaning for public health a certain rigor must be applied to their use. Per the Working Group definition a “biomarker” should be “a characteristic that is objectively measured” and to that end the assay used to measure it should be robust and validated for performance characteristics. Research in many laboratories, including ours, focuses on potential biomarkers, but that distinction should not be forgotten. Furthermore, the biomarker should be “an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention”; the implication is that the context of use need be explicitly defined. This is the process of qualification, to be distinguished from analytical validation. To be truly “translational” a biomarker needs to satisfy the above criteria and be qualified in at least two experimental settings, such as measuring liver injury in rodents and in humans. Of course, that means the assay must be validated for performance in the biological media obtained from the different settings. More difficult for the translational qualification is the reality that experimental designs in non-clinical and clinical investigations are too often vastly different. Approaches to address these challenges and examples will be discussed.


5:20 Understanding IMiDS: Mechanism, Differentiation and BiomarkersPatrick R. Hagner, Ph.D., Scientist, Translational Development, Celgene




THURSDAY, MAY 7


Sponsored by


Biomarker Assay Development and Validation8:25 Chairperson’s RemarksKen Chang, Ph.D., Clinical Assay Development & Outsourcing Lead, Merck

8:30 Development and Validation of a Clinical Biomarker Assay to Quantitate Thymic Stromal Lymphopoietin in Human Plasma at Sub-pg/mL levelXuemei Zhao, Ph.D., Principal Scientist, Molecular Biomarkers and Diagnostics Laboratory, MerckTSLP is an attractive therapeutic target for the treatment of allergic diseases, and plasma TSLP is a potential biomarker in the development of therapeutic agents. We developed and validated an ultra-sensitive electrochemiluminescence assay for measurement of TSLP in plasma with a lower limit of quantitation of 0.12 pg/mL, which allowed the quantitation of TSLP in approximately 90% of human plasma samples tested. The assay demonstrated excellent performance characteristics. The validated TSLP assay enables assessment of circulating TSLP as a patient selection marker in the development of therapeutics to treat atopic diseases.

8:55 Fit-For-Purpose in situ Analytical Validation of NGS Mutation Profiling in FFPE TissueKen Chang, Ph.D., Clinical Assay Development & Outsourcing Lead, MerckWe have developed a “Concordance Calculator” to quantify reproducibility of multi-variant calls among Next-Generation Sequencing (NGS) replicates (same gDNA with different library preparations). This novel approach also allowed us to eliminate many different technical artifacts including Post Tissue Collection Modifications (PTCM) such as deamination and oxidation artifacts. We then developed a “Fit-for-Purpose in situ analytical validation” strategy using RainDance ThunderBolts Cancer Panel to include part of the analytical validation directly on each and every clinical sample. This strategy also involves using a set of normal FFPE tissue samples to eliminate panel/library prep/pipeline specific artifacts. The detail of this novel analytical validation approach will be discussed in detail.

9:20 SOMAmer® Reagents and the SOMAscanTM Assay, Tools for Real-Time Biology

Sponsored by

Andy Keys, Associate Director, Sales, North America, SomaLogicSomaLogic’s proteomic tools have found broad success in R&D applications including: biomarker discovery and diagnostics development, target validation in pre-clinical and clinical research; pharmacology in cells, tissues, and clinical samples; and custom assay development. We offer tools from broad biomarker discovery to developing single detection reagents.

9:35 The Impact of Preanalytical Variables on Biomarker Research

Sponsored by

David Craft, Ph.D., Senior Manager Sciences, Preanalytical Systems, Becton Dickson & CompanyThe use of biomarkers can potentially improve the efficiency of the drug development process. The preanalytical phase has great potential for errors. This presentation will focus on the potential impact of sample handling on RNA, proteins, cells within blood / tissue and how this variability can be controlled.


Genomic Biomarker Discovery10:45 Discover Genomic Biomarkers for Assisting Vaccine Research and DevelopmentI-Ming Wang, Ph.D., Principal Scientist, Genetics and Pharmacogenomics, Merck Research LabsThis presentation describes our integrated analysis of immune response to infection and vaccination by a genome-wide blood gene expression approach. Our main goal is to determine prediction rules governing the immune system’s behavior under different conditions. Proof-of-concept human and non-human primate genomic studies were conducted to identify potential accessible biomarkers for predicting vaccine response/safety and disease susceptibility to infection. Harvesting results from these efforts and applying them in the clinical setting should significantly enhance our capacity for future vaccine development.

11:10 Drug Target Validation in Concert with Clinical DevelopmentLiling Warren, Ph.D., Senior Scientific Investigator, GlaxoSmithKline

11:35 Novel Biomarker Approaches for Pathologic Angiogenesis in Human CancersAejaz Nasir, M.D., MPhil, Fellow, College of American Pathologists; Senior Medical Advisor & Surgical Pathology Lead, Molecular Solid Tumor & Anatomic Pathologist, Tailored Therapeutics, Diagnostic & Experimental Pathology, Eli Lilly and Company

12:00 pm Luncheon Presentation: Reagent Qualification and Platform Selection Considerations for Single and Multiplex Biomarker Analysis in Support of Clinical Studies

Sponsored by

Afshin Safavi, Ph.D., Founder and CSO, BioAgilytix LabsBiomarker analysis has become a common practice by many pharmaceutical companies to support PK/PD modeling. The reliability of outcomes is heavily influenced by the quality of the reagents and commercial kits as well as the selection of bioanalytical platform. Case studies will be presented to highlight the key bioanalytical considerations involved in running successful biomarker analyses in support of clinical studies with consideration to platform selection and critical reagents as well as kit selection.

Partnering and Collaborations1:30 Chairperson’s Opening RemarksGeorge A. Green IV, Ph.D., Group Director, Pharmacodiagnostic Center of Excellence, Bristol-Myers Squibb


1:35 Creating and Managing the Multiple Interfaces of Drug/Diagnostic Co-DevelopmentGeorge A. Green IV, Ph.D., Group Director, Pharmacodiagnostic Center of Excellence, Bristol-Myers SquibbAndrea H. Lauber, Ph.D., Executive Director, Business Development, Clinical Biomarkers and Pharmacodiagnostics, Bristol-Myers SquibbMany pharmaceutical companies are using an external partnering model to pursue co-development of drugs and diagnostic products. This approach provides access to diverse biomarkers, technology and platforms, as well as diagnostic manufacturing and commercialization expertise, thus maximizing diagnostic development capabilities. External partnering creates multiple interfaces of functions both within and between the drug and diagnostic companies. We will explore some of the challenges that accompany these interfaces, their management and implications, along with ideas for optimizing the “virtual diagnostic company” model for the Rx/Dx co-development environment.

2:25 Innovative Strategies and Progress in Translational Biomarkers in Clinical Oncology through Public-Private PartnershipsPaula Eason, Ph.D., Scientific Program Manager, Cancer Division of Research Partnerships, Foundation for the National Institutes of HealthThe continual need for development of biomarkers with robust clinical utility is an ongoing challenge for all cancer types. Incorporation of prognostic and predictive biomarkers into clinical trial strategies and therapeutic decision-making is essential to disentangle the complexities of the pathogenic process, drug pharmacodynamics, and tumor heterogeneity. Success will require strategic partnerships and alliances between public and private sectors to share resources, risks, experience and expertise, and to align multiple stakeholder incentives to support and accelerate sustainable innovation.



Clinical NGS Testing

M AY 6 - 7

WEDNESDAY, MAY 6


12:15 pm Luncheon Presentation: Enriching Nucleic Acids for Next-Generation Sequencing Analyses of SNPs, CNVs, Gene Fusions and More

Sponsored by

Joe Don Heath, Ph.D., Vice President, Market Development Diagnostics, NuGENThe novel Single Primer Enrichment Technology (SPET) and how it differs from existing target enrichment methods will be described. Sensitive variant detection from genomic DNA derived from fresh and FFPE tissues using 344 cancer-related genes will be demonstrated as well as utilization of SPET as a rapid, cost-effective screening tool for discovery of novel fusions and detection of known fusions with a panel of 500 cancer genes implicated in fusions events.

NGS in the Clinic1:30 Chairperson’s Opening RemarksNikoletta Sidiropoulos, M.D., Medical Director, Genomic Medicine Program, University of Vermont

1:35 Using Genome Sequencing in the Clinical SettingJason Merker, M.D., Ph.D., Assistant Professor, Pathology, Stanford University Medical CenterGenome sequencing is increasingly being applied in clinical practice for the diagnosis of unexplained heritable disease. I will describe our experience with establishing a clinical genomics service at an academic medical center. I will then discuss the benefits and challenges identified during our initial efforts to use genome sequencing to identify the molecular etiology in patients with unexplained hereditary cancer risk.

2:00 The Realities of Implementing Clinical Genomic Testing: The Good, the Bad and the UglyNikoletta Sidiropoulos, M.D., Medical Director, Genomic Medicine Program, University of VermontOptimizing the implementation of clinical genomic testing goes much beyond rigorous test validation. Generating genomic information and integrating it into clinical care requires collaboration between several divisions within the laboratory, clinicians, both physicians and ancillary care providers, as well as bioinformaticians, computational biologists, and information systems experts. This presentation will address key logistical elements that should be considered in an effort to optimize the clinical implementation of genomic medicine.

2:25 Laboratory-Developed Tests in the Genomic Medicine Era: Validation, Regulation and Challenges Faced by New Technologies and Clinical ApplicationsAndrea Ferreira-Gonzalez, Ph.D., Professor and Chair, Division of Molecular Diagnostics; Director, Molecular Diagnostics Laboratory, Department of Pathology, Virginia Commonwealth UniversityLaboratory-developed tests are those tests developed, validated and performed by clinical laboratories. There are standards and regulations in place for the validation of these tests before they are introduced into clinical practice. This presentation will discuss the process of validation under the current regulatory framework, and regulatory challenges posed by new technologies such as NGS and its clinical applications.

2:50 Clinical NGS: Moving from Gene Panels to Exome SequencingBirgit Funke, Ph.D., Assistant Professor, Pathology, MGH/Harvard Medical School; Director, Clinical Research and Development, Laboratory for Molecular Medicine, Partners HealthCareNGS is increasingly used in the clinic, most commonly in the form of targeted gene panels that are custom tailored for specific diseases. This paradigm cannot keep up with the accelerating pace of novel discoveries, making static gene panels suboptimal for many disorders. As the quality of exome capture kits is improving, the nature of targeted panels is beginning to change from a static, stand-alone assay to a set of genes that is interrogated from an underlying exome assay.


4:25 Clinical Impact of NGS Multi-Gene Panels in Diagnosis and Management of Hereditary Cancer SyndromesJames M. Ford, M.D., Associate Professor, Medicine (Oncology) and Genetics, and Director, Stanford Clinical Cancer Genomics Program, Stanford University School of MedicineNext-generation sequencing-based panels assaying multiple hereditary cancer risk genes are entering clinical use; however, little is known about their yield or effect on clinical management of patients. We have sequenced germline DNA samples from over 400 patients with personal and family histories of breast and ovarian cancer, but without BRCA1/2 mutations, and found ~10% carry potentially pathogenic mutations in other cancer susceptibility genes. Challenges include return of genetic information to patients, clinical management, screening and risk-reducing interventions in individuals with mutations in moderate-penetrance genes and high-penetrance genes in non-syndromic families, and incidental findings.

4:50 Clinical NGS for Solid Tumor TestingRajyalakshmi Luthra, Ph.D., Director, Molecular Diagnostic Laboratory; Professor, Pathology and Laboratory Medicine, MD Anderson Cancer Center

5:15 Defining Clinical Utility for Genomic Testing Supported by

Elaine Lyon, Ph.D., Medical Director, Molecular Genetics and Genomics, ARUP Laboratories; Associate Professor, University of Utah School of Medicine; Past President, Association for Molecular PathologyIn addition to showing analytical and clinical validity, clinical laboratories are being asked to demonstrate clinical utility, or how their tests are useful in treating or managing disease. Traditional models such as large case/control studies are not feasible for rare variants identified by genomic sequencing. Alternative methods and models are needed to establish appropriate standards for molecular tests. This presentation will discuss unique challenges for molecular tests, and the need for novel solutions.





THURSDAY, MAY 7


Sponsored by


NGS-Driven Clinical Trials8:25 Chairperson’s RemarksDaniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling Core, National Cancer Institute, NIH

8:30 MSK-IMPACT: Clinical Experience with High Volume Hybrid Capture-Based Next-Generation Sequencing to Enable Personalized Oncology and Prepopulate Genetically Informed Clinical TrialsMarc Ladanyi, M.D., William Ruane Chair in Molecular Oncology, Molecular Diagnostics Service and Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center

8:55 Bringing the Power of Genomics and Next-Generation Sequencing to the NCI Clinical TrialsDaniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling Core, National Cancer Institute, NIH

9:20 Purpose-built Targeted Sequencing Technology to Discover Gene Fusions, SNPs and CNVs in Clinically Relevant Samples

Supported by

Thon de Boer, Ph.D., Technical Product Manager, ArcherDX, Inc.Anchored Multiplex PCR (AMP™) is a target enrichment technology for NGS-based biomarker discovery. AMP accurately detects germline and somatic mutations such as gene fusions, SNPs, indels, and copy number changes from as little as 80pg total nucleic acid. This talk will highlight the various applications of AMP and the companion analysis software that enables detection of various gene fusions down to 0.1% simulated tumor cellularity.


10:45 Opportunities and Challenges for NGS-Based Clinical TrialsJamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity (an MPLN company)The requirements and challenges for NGS-based diagnostics are different from those for NGS-based clinical trials. The evolving technology and regulatory landscapes present increased opportunity for utilizing NGS in clinical trials; however, a thorough understanding of workflow challenges, technical limitations and data analysis is required for optimal success. The key challenges in NGS-based clinical trials will be discussed, and opportunities around assay validation, companion diagnostics, data analysis, genomic annotation and supporting services will be highlighted.

11:10 Considerations for the Use of Comprehensive Genomic Profiling in Oncology Clinical Care and Clinical TrialsMatthew Hawryluk, Ph.D., Senior Director, Corporate & Business Development, Foundation Medicine IncOncology has engaged cancer as a disease of the genome, informed by an increased understanding of the genomic alterations that drive patient tumors. Foundation Medicine addressed the scientific, technical and practical challenges

in developing a comprehensive cancer genomic profiling test based on next-generation sequencing (NGS), enabling the development of targeted therapies in the trial setting and helping appropriately identify patients in routine care. The approach advances novel treatment paradigms and accelerates progress toward truly personalized medicine.

11:35 Supporting Clinical Trials and Clinical Decision-Making through Genomic SequencingJennifer J.D. Morrissette, Ph.D., Clinical Director, Center for Personalized Diagnostics, University of Pennsylvania School of MedicineRapid advancements in next-generation sequencing (NGS) have opened the door for unprecedented diagnostic capabilities. While these technologies make it feasible to sequence large genomic regions in very short periods of time, the overall utility is limited by the variety of targets and validation of custom assays to support immediate clinical needs. This presentation will focus on the clinical utility of genomic testing and will highlight two areas of impact. The first section will highlight the impact of genomic mutation detection on patient care and decision making. The second section will focus on the laboratory effort to support clinical trials, including the development of an NGS assay to support the chimeric antigen receptor T-cell directed therapy (CAR T) for EGFRvIII to identify appropriate patients with glioblastoma multiforma for inclusion.

12:00 pm Enjoy Lunch on Your Own

NGS Assay Development and Platforms1:30 Chairperson’s Opening RemarksSeth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of Medicine

1:35 Development of Clinical Sequencing Assays: Analytical Validation ApproachesSaumya Pant, Ph.D., Senior Research Investigator and Head, Sequencing Technologies, Bristol-Myers Squibb

2:00 Detection of Variants in Cardiomyopathies and Arrhythmias: Validation and Case StudiesSeth Crosby, M.D., Director, Partnerships & Alliances, Washington University School of MedicineWe detect genetic variants underlying nine myocardial phenotypes with often overlapping and/or subtle presentations. Testing is executed from a validated clinical exome (Agilent Clinical Research Exome). Data analysis and visualization are performed using a WashU developed computational suite, Clinical Genomics Workstation. I will review the design, validation and experience with this new assay.

2:25 Different Next-Generation Sequencing Platforms and Their Clinical UtilityDavid Smith, Ph.D., Professor, Laboratory Medicine & Pathology, Mayo ClinicNext-generation sequencing (NGS) is a powerful technology that utilizes massively parallel sequencing to analyze many millions of DNA molecules simultaneously. The first NGS platform was developed by 454 in 2005, but this was quickly eclipsed by the Illumina sequencing platform. Today there are a number of different NGS platforms including Illumina, Ion Torrent and Pacific Biosciences. There are also numerous new NGS technologies being developed. In this presentation I will talk about the various NGS platforms and discuss their strengths and weaknesses. Then, I will discuss the clinical applications of these platforms and how these powerful technologies will totally transform the way we clinically manage cancer patients.



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May 5-6, 2015 May 6-7, 2015T1: Biomarkers for Patient Selection T5: Companion Diagnostics T2: Big Data for Personalized Medicine and Biomarker Discovery T6: Clinical and Translational Biomarkers in Drug DiscoveryT3: Cell-Free Biomarkers and Diagnostics T7: Clinical NGS TestingT4: Predictive Cancer Biomarkers

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